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Error in using cg_bonds.tcl
- Logan
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1) Take xx.pdb file from Protein Data Bank
2) ./martinize.py -f xx.pdb -o system.top -x cg_xx.pdb -ff martini21 -ss xx.dssp -elastic (here xx.dssp is taken from www.cmbi.ru.nl/hsspsoap/ by using xx.pdb downloaded in the previous step)
3) In VMD, sourcing and cg_bonds -top system.top
This works for some proteins to show elastic network in VMD but mostly not working with the error "invalid atom id"
Could you please let me know what is the problem.
Thanks
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- Clement
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Then, this script seems to be... unstable with the topologies written with martinize.py. Comes from the order bond/constraints are read. I wrote another script to do exactly the same thing, but in a most robust way; it's going to be released at some point.
Note that if you want to use an elastic network on your protein, we recommend ElNeDyn... Flag -ff elnedyn in martinize.py I believe.
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- Logan
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I tried things you recommended but it did not work through.
cg_bonds -top system.top -topoltype "elastic" still generated error message of "invalid atom id" with both -ff elnedyn and -ff martini21 in using martinize.py
Could you recommend any other script for generating CG model of PDB protein?
Best,
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- Clement
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- Logan
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- Clement
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- Xotic
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- bart
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cgmartini.nl/images/tools/VMD/cg_bonds-v5.tcl
Then with this I usually do the following which works for an extreme wide range of tested protein and dsDNA models using elastic networks.
1) load gro, xtc (or only gro)
2) type in the vmd command line:
cg_bonds -topoltype "elnedyn" -color "orange" -mat "AOChalky" -res 52 -rad 0.2 -top ./topol.top
3) if you have too many bonds to be drawn in VMD (a problem due to the AA focus of VMD), you can add -cutoff 7.5 (works almost all the time) for showing the bonds, though you are now not showing all bonds, which might or might not be considered cheating. You can get around this by asking for a special build on the VMD mailing list which has a higher maximum value of bonds per atom.
This assumes that the topology file is in the same folder as the currently active folder in VMD. You can just change directories using the VMD terminal until this is true, or open VMD in the folder containing the topol. It is important to prepend it with ./ otherwise you get a pointing error in VMD, which might or might not be clear at all (this should all be true for VMD version >= 1.9.3).
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- aguljas
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- riccardo
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echo 0 | gmx trjconv -f run.gro -s run.tpr -conect -o run-conect.pdb -pbc whole
sed -i '/ENDMDL/d' run-conect.pdb
And then:
vmd run-conect.pdb
vmd run-conect.pdb traj.xtc
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- bart
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- buuhuu
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- bart
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- bqAlvii
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echo 0 | gmx trjconv -f run.gro -s run.tpr -conect -o run-conect.pdb -pbc whole
sed -i '/ENDMDL/d' run-conect.pdb
EDIT
I notice that the command was functionally perfect, just one extra space in sed editor generate the error.
Nothing wrong with the command. Thanks you all anyways.
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